[package - head-amd64-default][biology/gmap] Failed for gmap-2015.09.21 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Mon Aug 31 02:30:52 UTC 2020
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb at FreeBSD.org
Last committer: linimon at FreeBSD.org
Ident: $FreeBSD: head/biology/gmap/Makefile 504785 2019-06-21 11:15:08Z linimon $
Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p546860_s364942/logs/gmap-2015.09.21.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p546860_s364942
Log:
=>> Building biology/gmap
build started at Mon Aug 31 02:27:32 UTC 2020
port directory: /usr/ports/biology/gmap
package name: gmap-2015.09.21
building for: FreeBSD head-amd64-default-job-14 13.0-CURRENT FreeBSD 13.0-CURRENT 1300113 amd64
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/gmap/Makefile 504785 2019-06-21 11:15:08Z linimon $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300100
Jail OSVERSION: 1300113
Job Id: 14
!!! Jail is newer than host. (Jail: 1300113, Host: 1300100) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> Use 'make config' to modify these settings
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jwb at FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GMAP accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> gmap-2015.09.21 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.7.txz
[head-amd64-default-job-14] Installing pkg-1.14.7...
[head-amd64-default-job-14] Extracting pkg-1.14.7: .......... done
===> gmap-2015.09.21 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gmap-2015.09.21
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GMAP accepted by the user
===> Fetching all distfiles required by gmap-2015.09.21 for building
===========================================================================
=======================<phase: checksum >============================
===> License GMAP accepted by the user
===> Fetching all distfiles required by gmap-2015.09.21 for building
=> SHA256 Checksum OK for gmap-gsnap-2015-09-21.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GMAP accepted by the user
===> Fetching all distfiles required by gmap-2015.09.21 for building
===> Extracting for gmap-2015.09.21
=> SHA256 Checksum OK for gmap-gsnap-2015-09-21.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for gmap-2015.09.21
===========================================================================
=======================<phase: build-depends >============================
===> gmap-2015.09.21 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.txz
[head-amd64-default-job-14] Installing gmake-4.3_2...
[head-amd64-default-job-14] `-- Installing gettext-runtime-0.21...
[head-amd64-default-job-14] | `-- Installing indexinfo-0.3.1...
[head-amd64-default-job-14] | `-- Extracting indexinfo-0.3.1: .... done
[head-amd64-default-job-14] `-- Extracting gettext-runtime-0.21: .......... done
[head-amd64-default-job-14] Extracting gmake-4.3_2: .......... done
<snip>
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-access.o -MD -MP -MF .deps/atoiindex-access.Tpo -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c
mv -f .deps/atoiindex-bigendian.Tpo .deps/atoiindex-bigendian.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-univinterval.o -MD -MP -MF .deps/atoiindex-univinterval.Tpo -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
mv -f .deps/atoiindex-univinterval.Tpo .deps/atoiindex-univinterval.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-interval.o -MD -MP -MF .deps/atoiindex-interval.Tpo -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/atoiindex-access.Tpo .deps/atoiindex-access.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-filestring.o -MD -MP -MF .deps/atoiindex-filestring.Tpo -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
mv -f .deps/atoiindex-interval.Tpo .deps/atoiindex-interval.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-iit-read-univ.o -MD -MP -MF .deps/atoiindex-iit-read-univ.Tpo -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
mv -f .deps/atoiindex-filestring.Tpo .deps/atoiindex-filestring.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-iit-read.o -MD -MP -MF .deps/atoiindex-iit-read.Tpo -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/atoiindex-iit-read-univ.Tpo .deps/atoiindex-iit-read-univ.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-compress.o -MD -MP -MF .deps/atoiindex-compress.Tpo -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/atoiindex-compress.Tpo .deps/atoiindex-compress.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-compress-write.o -MD -MP -MF .deps/atoiindex-compress-write.Tpo -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
mv -f .deps/atoiindex-compress-write.Tpo .deps/atoiindex-compress-write.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-popcount.o -MD -MP -MF .deps/atoiindex-popcount.Tpo -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
mv -f .deps/atoiindex-popcount.Tpo .deps/atoiindex-popcount.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-genome128_hr.o -MD -MP -MF .deps/atoiindex-genome128_hr.Tpo -c -o atoiindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
mv -f .deps/atoiindex-iit-read.Tpo .deps/atoiindex-iit-read.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-bitpack64-read.o -MD -MP -MF .deps/atoiindex-bitpack64-read.Tpo -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/atoiindex-bitpack64-read.Tpo .deps/atoiindex-bitpack64-read.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-bitpack64-readtwo.o -MD -MP -MF .deps/atoiindex-bitpack64-readtwo.Tpo -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
mv -f .deps/atoiindex-genome128_hr.Tpo .deps/atoiindex-genome128_hr.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-bitpack64-write.o -MD -MP -MF .deps/atoiindex-bitpack64-write.Tpo -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
mv -f .deps/atoiindex-bitpack64-readtwo.Tpo .deps/atoiindex-bitpack64-readtwo.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-indexdb.o -MD -MP -MF .deps/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
mv -f .deps/atoiindex-indexdb.Tpo .deps/atoiindex-indexdb.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-indexdb-write.o -MD -MP -MF .deps/atoiindex-indexdb-write.Tpo -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb-write.c:1189:67: warning: format specifies type 'intmax_t' (aka 'long') but the argument has type 'Positionsptr_T' (aka 'unsigned int') [-Wformat]
fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(unsigned char),offset);
~~~ ^~~
%u
indexdb-write.c:1201:67: warning: format specifies type 'intmax_t' (aka 'long') but the argument has type 'Positionsptr_T' (aka 'unsigned int') [-Wformat]
fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(UINT4),offset);
~~~ ^~~
%u
indexdb-write.c:2328:22: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat]
positionsfile_high,totalcounts*sizeof(unsigned char),filesize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
indexdb-write.c:2343:24: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat]
positionsfile_high,totalcounts*sizeof(unsigned char),filesize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
indexdb-write.c:2350:21: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat]
positionsfile_low,totalcounts*sizeof(UINT4),filesize);
^~~~~~~~~~~~~~~~~~~~~~~~~
indexdb-write.c:2365:23: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat]
positionsfile_low,totalcounts*sizeof(UINT4),filesize);
^~~~~~~~~~~~~~~~~~~~~~~~~
indexdb-write.c:2408:21: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat]
positionsfile_low,totalcounts*sizeof(UINT4),filesize);
^~~~~~~~~~~~~~~~~~~~~~~~~
indexdb-write.c:2423:23: warning: format specifies type 'size_t' (aka 'unsigned long') but the argument has type 'unsigned long long' [-Wformat]
positionsfile_low,totalcounts*sizeof(UINT4),filesize);
^~~~~~~~~~~~~~~~~~~~~~~~~
8 warnings generated.
mv -f .deps/atoiindex-indexdb-write.Tpo .deps/atoiindex-indexdb-write.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-atoi.o -MD -MP -MF .deps/atoiindex-atoi.Tpo -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/atoiindex-bitpack64-write.Tpo .deps/atoiindex-bitpack64-write.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-md5.o -MD -MP -MF .deps/atoiindex-md5.Tpo -c -o atoiindex-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/atoiindex-md5.Tpo .deps/atoiindex-md5.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-bzip2.o -MD -MP -MF .deps/atoiindex-bzip2.Tpo -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/atoiindex-bzip2.Tpo .deps/atoiindex-bzip2.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-sequence.o -MD -MP -MF .deps/atoiindex-sequence.Tpo -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/atoiindex-atoi.Tpo .deps/atoiindex-atoi.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-genome.o -MD -MP -MF .deps/atoiindex-genome.Tpo -c -o atoiindex-genome.o `test -f 'genome.c' || echo './'`genome.c
mv -f .deps/atoiindex-sequence.Tpo .deps/atoiindex-sequence.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-uintlist.o -MD -MP -MF .deps/atoiindex-uintlist.Tpo -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/atoiindex-uintlist.Tpo .deps/atoiindex-uintlist.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-intlist.o -MD -MP -MF .deps/atoiindex-intlist.Tpo -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/atoiindex-intlist.Tpo .deps/atoiindex-intlist.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-saca-k.o -MD -MP -MF .deps/atoiindex-saca-k.Tpo -c -o atoiindex-saca-k.o `test -f 'saca-k.c' || echo './'`saca-k.c
mv -f .deps/atoiindex-saca-k.Tpo .deps/atoiindex-saca-k.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-uint8list.o -MD -MP -MF .deps/atoiindex-uint8list.Tpo -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
uint8list.c:268:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
sprintf(Buffer,"%u,",Uint8list_head(p));
~~ ^~~~~~~~~~~~~~~~~
%llu
uint8list.c:271:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
sprintf(Buffer,"%u",Uint8list_head(p));
~~ ^~~~~~~~~~~~~~~~~
%llu
uint8list.c:277:28: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
sprintf(Buffer,"%u,",Uint8list_head(p));
~~ ^~~~~~~~~~~~~~~~~
%llu
uint8list.c:280:25: warning: format specifies type 'unsigned int' but the argument has type 'UINT8' (aka 'unsigned long long') [-Wformat]
sprintf(Buffer,"%u",Uint8list_head(p));
~~ ^~~~~~~~~~~~~~~~~
%llu
4 warnings generated.
mv -f .deps/atoiindex-uint8list.Tpo .deps/atoiindex-uint8list.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-bytecoding.o -MD -MP -MF .deps/atoiindex-bytecoding.Tpo -c -o atoiindex-bytecoding.o `test -f 'bytecoding.c' || echo './'`bytecoding.c
mv -f .deps/atoiindex-bytecoding.Tpo .deps/atoiindex-bytecoding.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-sarray-write.o -MD -MP -MF .deps/atoiindex-sarray-write.Tpo -c -o atoiindex-sarray-write.o `test -f 'sarray-write.c' || echo './'`sarray-write.c
sarray-write.c:530:65: warning: format specifies type 'unsigned int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace);
~~ ^~~~~~~~~
%llu
sarray-write.c:530:75: warning: format specifies type 'unsigned int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace);
~~ ^~~~~~~~~~
%llu
sarray-write.c:634:65: warning: format specifies type 'unsigned int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace);
~~ ^~~~~~~~~
%llu
sarray-write.c:634:75: warning: format specifies type 'unsigned int' but the argument has type 'Oligospace_T' (aka 'unsigned long long') [-Wformat]
fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace);
~~ ^~~~~~~~~~
%llu
sarray-write.c:2273:62: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
Genome_fill_buffer_simple(genomecomp,/*left*/0,/*length*/n,gbuffer);
^~~~~~~
./genome.h:49:77: note: passing argument to parameter 'gbuffer1' here
Genome_fill_buffer_simple (T this, Univcoord_T left, Chrpos_T length, char *gbuffer1);
^
sarray-write.c:2391:62: warning: passing 'unsigned char *' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
Genome_fill_buffer_simple(genomecomp,/*left*/0,/*length*/n,gbuffer);
^~~~~~~
./genome.h:49:77: note: passing argument to parameter 'gbuffer1' here
Genome_fill_buffer_simple (T this, Univcoord_T left, Chrpos_T length, char *gbuffer1);
^
6 warnings generated.
mv -f .deps/atoiindex-sarray-write.Tpo .deps/atoiindex-sarray-write.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-list.o -MD -MP -MF .deps/atoiindex-list.Tpo -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/atoiindex-list.Tpo .deps/atoiindex-list.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-datadir.o -MD -MP -MF .deps/atoiindex-datadir.Tpo -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/atoiindex-genome.Tpo .deps/atoiindex-genome.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-getopt.o -MD -MP -MF .deps/atoiindex-getopt.Tpo -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/atoiindex-datadir.Tpo .deps/atoiindex-datadir.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-getopt1.o -MD -MP -MF .deps/atoiindex-getopt1.Tpo -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/atoiindex-getopt1.Tpo .deps/atoiindex-getopt1.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT atoiindex-atoiindex.o -MD -MP -MF .deps/atoiindex-atoiindex.Tpo -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c
mv -f .deps/atoiindex-getopt.Tpo .deps/atoiindex-getopt.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-except.o -MD -MP -MF .deps/sam_sort-except.Tpo -c -o sam_sort-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/sam_sort-except.Tpo .deps/sam_sort-except.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-assert.o -MD -MP -MF .deps/sam_sort-assert.Tpo -c -o sam_sort-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/sam_sort-assert.Tpo .deps/sam_sort-assert.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-mem.o -MD -MP -MF .deps/sam_sort-mem.Tpo -c -o sam_sort-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/sam_sort-mem.Tpo .deps/sam_sort-mem.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-littleendian.o -MD -MP -MF .deps/sam_sort-littleendian.Tpo -c -o sam_sort-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/sam_sort-littleendian.Tpo .deps/sam_sort-littleendian.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-bigendian.o -MD -MP -MF .deps/sam_sort-bigendian.Tpo -c -o sam_sort-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/sam_sort-bigendian.Tpo .deps/sam_sort-bigendian.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-intlist.o -MD -MP -MF .deps/sam_sort-intlist.Tpo -c -o sam_sort-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/atoiindex-atoiindex.Tpo .deps/atoiindex-atoiindex.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-list.o -MD -MP -MF .deps/sam_sort-list.Tpo -c -o sam_sort-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/sam_sort-list.Tpo .deps/sam_sort-list.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-stopwatch.o -MD -MP -MF .deps/sam_sort-stopwatch.Tpo -c -o sam_sort-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/sam_sort-intlist.Tpo .deps/sam_sort-intlist.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-access.o -MD -MP -MF .deps/sam_sort-access.Tpo -c -o sam_sort-access.o `test -f 'access.c' || echo './'`access.c
mv -f .deps/sam_sort-stopwatch.Tpo .deps/sam_sort-stopwatch.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-univinterval.o -MD -MP -MF .deps/sam_sort-univinterval.Tpo -c -o sam_sort-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
mv -f .deps/sam_sort-univinterval.Tpo .deps/sam_sort-univinterval.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-interval.o -MD -MP -MF .deps/sam_sort-interval.Tpo -c -o sam_sort-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/sam_sort-access.Tpo .deps/sam_sort-access.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-uintlist.o -MD -MP -MF .deps/sam_sort-uintlist.Tpo -c -o sam_sort-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/sam_sort-interval.Tpo .deps/sam_sort-interval.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-filestring.o -MD -MP -MF .deps/sam_sort-filestring.Tpo -c -o sam_sort-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
mv -f .deps/sam_sort-uintlist.Tpo .deps/sam_sort-uintlist.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-iit-read-univ.o -MD -MP -MF .deps/sam_sort-iit-read-univ.Tpo -c -o sam_sort-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
mv -f .deps/sam_sort-filestring.Tpo .deps/sam_sort-filestring.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-iit-read.o -MD -MP -MF .deps/sam_sort-iit-read.Tpo -c -o sam_sort-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/sam_sort-iit-read-univ.Tpo .deps/sam_sort-iit-read-univ.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-samheader.o -MD -MP -MF .deps/sam_sort-samheader.Tpo -c -o sam_sort-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
mv -f .deps/sam_sort-samheader.Tpo .deps/sam_sort-samheader.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-samread.o -MD -MP -MF .deps/sam_sort-samread.Tpo -c -o sam_sort-samread.o `test -f 'samread.c' || echo './'`samread.c
mv -f .deps/sam_sort-samread.Tpo .deps/sam_sort-samread.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-datadir.o -MD -MP -MF .deps/sam_sort-datadir.Tpo -c -o sam_sort-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/sam_sort-datadir.Tpo .deps/sam_sort-datadir.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-getopt.o -MD -MP -MF .deps/sam_sort-getopt.Tpo -c -o sam_sort-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/sam_sort-getopt.Tpo .deps/sam_sort-getopt.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-getopt1.o -MD -MP -MF .deps/sam_sort-getopt1.Tpo -c -o sam_sort-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/sam_sort-getopt1.Tpo .deps/sam_sort-getopt1.Po
cc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -pthread -DGMAPDB=\"/usr/local/share\" -DUTILITYP=1 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT sam_sort-sam_sort.o -MD -MP -MF .deps/sam_sort-sam_sort.Tpo -c -o sam_sort-sam_sort.o `test -f 'sam_sort.c' || echo './'`sam_sort.c
mv -f .deps/sam_sort-iit-read.Tpo .deps/sam_sort-iit-read.Po
/bin/sh ../libtool --tag=CC --mode=link cc -D_THREAD_SAFE -pthread -DTARGET=\"amd64-portbld-freebsd13.0\" -DGMAPDB=\"/usr/local/share\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-filestring.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-order
stat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-output.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm
libtool: link: cc -D_THREAD_SAFE -pthread -DTARGET=\"amd64-portbld-freebsd13.0\" -DGMAPDB=\"/usr/local/share\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-filestring.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-in
tron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-output.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm -pthread
ld: error: duplicate symbol: homopolymerp
>>> defined at dynprog_single.c
>>> gmap-dynprog_single.o:(homopolymerp)
>>> defined at dynprog_end.c
>>> gmap-dynprog_end.o:(.bss+0x38)
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[3]: *** [Makefile:1300: gmap] Error 1
gmake[3]: *** Waiting for unfinished jobs....
mv -f .deps/sam_sort-sam_sort.Tpo .deps/sam_sort-sam_sort.Po
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21/src'
gmake[2]: *** [Makefile:1195: all] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21/src'
gmake[1]: *** [Makefile:315: all-recursive] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/gmap/work/gmap-2015-09-21'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/gmap
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